It was kinda obvious that Yamato was going to be made redundant as soon as naruto figured out how to control kyuubi.
Seeing now that yamato's woody jutsu reacts to naruto, it should in turn mean that naruto would be a huge boost to Yamato. Recall the difference between light and dark jutsus that was briefly mentioned by kakashi but never got a lecture on it. Well there it is, naruto would dramatically boost light jutsu users.
This becomes an obvious setup for the final chapter where all the bijuus are there and yamato's woody element is not enough with out the boost of naruto.